#include <BALL/FORMAT/MOLFile.h>

Inheritance diagram for BALL::MOLFile:

Classes
class	AtomStruct

class	BondStruct

class	CountsStruct

struct	Property

Public Member Functions
Constructors and Destructors
	MOLFile ()

	MOLFile (const String &filename, File::OpenMode open_mode=std::ios::in)

virtual	~MOLFile ()
	Destructor. More...

Reading and Writing of Kernel Datastructures
virtual bool	write (const Molecule &molecule)

virtual bool	write (const System &system)

virtual bool	read (System &system)

virtual Molecule *	read ()

const MOLFile &	operator= (const MOLFile &file)

Public Member Functions inherited from BALL::GenericMolFile
	GenericMolFile ()

	GenericMolFile (const String &filename, File::OpenMode open_mode=std::ios::in)

virtual	~GenericMolFile ()

const GenericMolFile &	operator= (const GenericMolFile &rhs)

virtual GenericMolFile &	operator>> (System &system)

virtual GenericMolFile &	operator<< (const System &system)

virtual GenericMolFile &	operator>> (Molecule &molecule)

virtual GenericMolFile &	operator<< (const Molecule &molecule)

Public Member Functions inherited from BALL::LineBasedFile
	LineBasedFile ()
	Default constructor. More...

	LineBasedFile (const String &filename, File::OpenMode open_mode=std::ios::in, bool trim_whitespaces=false)

void	clear ()

bool	operator== (const LineBasedFile &f)

bool	operator!= (const LineBasedFile &f)

const LineBasedFile &	operator= (const LineBasedFile &file)

Position	getLineNumber () const
	Get the last line number in the file. More...

const String &	getLine () const
	Return the current line. More...

String &	getLine ()
	Return the current line. More...

bool	readLine ()

bool	skipLines (Size number=1)

bool	search (const String &text, bool return_to_start=false)

bool	search (const String &text, const String &stop, bool return_to_start=false)

bool	gotoLine (Position line_number)

void	rewind ()

void	test (const char *file, int line, bool condition, const String &msg) const

String	getField (Index pos=0, const String &quotes="", const String &delimiters=String::CHARACTER_CLASS__WHITESPACE) const

bool	startsWith (const String &text) const
	Test if the current line starts with text. More...

bool	has (const String &text) const
	Return true if the current line contains text. More...

Index	switchString (const std::vector< String > &data) const

bool	parseColumnFormat (const char format, Position index, Size length, void arg)

void	enableTrimWhitespaces (bool state)
	Set wheter leading and trailing whitespaces in lines shall be removed. More...

bool	trimWhiteSpacesEnabled () const

Public Member Functions inherited from BALL::File
	File ()

	File (const String &name, OpenMode open_mode=std::ios::in)

virtual	~File ()

bool	isValid () const

bool	open (const String &name, File::OpenMode open_mode=std::ios::in)

bool	reopen ()

bool	reopen (File::OpenMode open_mode)

void	close ()

const String &	getName () const

void	setName (const String &name)

const String &	getOriginalName () const

Size	getSize ()

File::OpenMode	getOpenMode () const

Type	getType (bool trace_link) const

bool	copyTo (const String &destination_name, Size buffer_size=4096)

bool	moveTo (const String &destination_name)

bool	remove ()

bool	renameTo (const String &new_path)

bool	truncate (Size size=0)

std::fstream &	getFileStream ()

TransformationManager &	getTransformationManager ()

const TransformationManager &	getTransformationManager () const

bool	operator== (const File &file) const

bool	operator!= (const File &file) const

bool	isOpen () const

bool	isClosed () const

bool	isAccessible () const

bool	isCanonized () const

bool	isReadable () const

bool	isWritable () const

bool	isExecutable () const

Protected Member Functions
Molecule *	readCTAB_ (std::vector< Atom * > &atom_map)

bool	readCountsLine_ (CountsStruct &counts)
	Read the Counts line of a MOL file. More...

bool	readAtomLine_ (AtomStruct &atom)
	Read a line from the atom block. More...

bool	readBondLine_ (BondStruct &bond)
	Read a line from the bond block. More...

void	writeCountsLine_ (const CountsStruct &counts)
	Write the Counts line. More...

void	writeAtomLine_ (const AtomStruct &atom)
	Write a line of the atom block. More...

void	writeBondLine_ (const BondStruct &bond)
	Write a line of the bond block. More...

Protected Member Functions inherited from BALL::GenericMolFile
virtual void	initRead_ ()

virtual void	initWrite_ ()

Static Protected Attributes
Format definitions
static const String	counts_format_
	The format of the counts line. More...

static const String	atom_format_
	The format of an entry of the atom block. More...

static const String	bond_format_
	The format of an entry of the bond block. More...

Additional Inherited Members
Public Types inherited from BALL::File
typedef std::ios::openmode	OpenMode

enum	Transformation { TRANSFORMATION__EXEC = 1, TRANSFORMATION__FILTER = 2, TRANSFORMATION__URL = 3 }

enum	Type { TYPE__UNKNOWN = 0, TYPE__DIRECTORY = 1, TYPE__CHAR_SPECIAL_FILE = 2, TYPE__BLOCK_SPECIAL_FILE = 3, TYPE__REGULAR_FILE = 4, TYPE__SYMBOLIC_LINK = 5, TYPE__SOCKET = 6, TYPE__FIFO_SPECIAL_FILE = 7 }

Static Public Member Functions inherited from BALL::File
static Size	getSize (String name)

static Type	getType (String name, bool trace_link)

static bool	copy (String source_name, String destination_name, Size buffer_size=4096)

static bool	move (const String &source_name, const String &destination_name)

static bool	remove (String name)

static bool	rename (String old_path, String new_path)

static bool	truncate (String path, Size size=0)

static bool	createTemporaryFilename (String &temporary, const String &suffix=".TMP")

static void	enableTransformation (Transformation transformation)

static void	disableTransformation (Transformation transformation)

static bool	isTransformationEnabled (Transformation transformation)

static void	registerTransformation (const String &pattern, const String &exec)

static void	unregisterTransformation (const String &pattern)

static bool	isAccessible (String name)

static bool	isReadable (String name)

static bool	isWritable (String name)

static bool	isExecutable (String name)

Static Public Attributes inherited from BALL::File
static const OpenMode	MODE_IN
	Open for input (default) More...

static const OpenMode	MODE_OUT
	Open for output. More...

static const OpenMode	MODE_APP
	Append. Seek to end before each write operation. More...

static const OpenMode	MODE_BINARY
	Binary mode. More...

static const OpenMode	MODE_ATE
	Seek to end directly after opening. More...

static const OpenMode	MODE_TRUNC
	Truncate an existing file. More...

static const String	TRANSFORMATION_EXEC_PREFIX
	Prefix for filenames that are created through the execution of commands "exec:". More...

static const String	TRANSFORMATION_FILE_PREFIX
	Prefix for files (to mimick URL-like behavior) "file:". More...

static const String	TRANSFORMATION_FTP_PREFIX
	Prefix for FTP-transfers "ftp://". More...

static const String	TRANSFORMATION_HTTP_PREFIX
	Prefix for HTTP-transfer "http://". More...

Protected Attributes inherited from BALL::LineBasedFile
String	line_
	buffer for the line in use More...

Position	line_number_
	line number in the file More...

bool	trim_whitespaces_

vector< char >	line_buffer_
	buffer for the line More...

vector< char >	col_buffer_
	buffer for column parsing More...

Detailed Description

MDL MOL file class. This class enables BALL to read and write MDL MOL files.

Definition at line 27 of file MOLFile.h.

Constructor & Destructor Documentation

BALL::MOLFile::MOLFile ( )

Default constructor

BALL::MOLFile::MOLFile	(	const String &	filename,
		File::OpenMode	open_mode = `std::ios::in`
	)

Detailed constructor.

Exceptions

Exception::FileNotFound if the file could not be opened

virtual BALL::MOLFile::~MOLFile ( )

virtual

Destructor.

Member Function Documentation

const MOLFile& BALL::MOLFile::operator= ( const MOLFile & file )

virtual bool BALL::MOLFile::read ( System & system )

virtual

Read a system from the MOL file

Exceptions

Exception::ParseError if a syntax error was encountered

Reimplemented from BALL::GenericMolFile.

Reimplemented in BALL::SDFile.

virtual Molecule* BALL::MOLFile::read ( )

virtual

Read a single molecule from the file

Exceptions

Exception::ParseError if a syntax error was encountered

Reimplemented from BALL::GenericMolFile.

Reimplemented in BALL::SDFile.

bool BALL::MOLFile::readAtomLine_ ( AtomStruct & atom )

protected

Read a line from the atom block.

bool BALL::MOLFile::readBondLine_ ( BondStruct & bond )

protected

Read a line from the bond block.

bool BALL::MOLFile::readCountsLine_ ( CountsStruct & counts )

protected

Read the Counts line of a MOL file.

Molecule* BALL::MOLFile::readCTAB_ ( std::vector< Atom * > & atom_map )

protected

Read the CTAB of a MOL file and construct a Molecule from its data

Exceptions

Exception::ParseError if a syntax error was encountered

virtual bool BALL::MOLFile::write ( const Molecule & molecule )

virtual

Write a molecule to the MOL file

Exceptions

File::CannotWrite if writing to the file failed

Reimplemented from BALL::GenericMolFile.

Reimplemented in BALL::SDFile.

virtual bool BALL::MOLFile::write ( const System & system )

virtual

Write a system to the MOL file.

Exceptions

File::CannotWrite if writing to the file failed

Reimplemented from BALL::GenericMolFile.

Reimplemented in BALL::SDFile.

void BALL::MOLFile::writeAtomLine_ ( const AtomStruct & atom )

protected

Write a line of the atom block.

void BALL::MOLFile::writeBondLine_ ( const BondStruct & bond )

protected

Write a line of the bond block.

void BALL::MOLFile::writeCountsLine_ ( const CountsStruct & counts )

protected

Write the Counts line.

Member Data Documentation

const String BALL::MOLFile::atom_format_

staticprotected

The format of an entry of the atom block.

Definition at line 177 of file MOLFile.h.

const String BALL::MOLFile::bond_format_

staticprotected

The format of an entry of the bond block.

Definition at line 180 of file MOLFile.h.

const String BALL::MOLFile::counts_format_

staticprotected

The format of the counts line.

Definition at line 174 of file MOLFile.h.

Classes

Public Member Functions

Protected Member Functions

Static Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation